"There are foreign fighters in those tribal areas who will have to be killed or captured," said Lt. Gen. David Barno, the commander of United States forces in Afghanistan on Monday.
The Pakistani government has offered an amnesty to foreign fighters in South Waziristan, a tribal region near the Afghan border where al-Qaida and Taliban members are believed to be living.
On Saturday, the government pushed back by one week a 30 April deadline for foreigners to surrender. Despite a threat of renewed military action, no foreign fighters have yet taken up the amnesty offer.
"It's very important that the Pakistani military continue with their operations to go after the foreign fighters in particular, who in my view will not be reconciled," Barno said at a news conference.
"We have some concerns that could go in the wrong direction," he said of the Pakistani operations.
Pakistan Army spokesman Maj Gen Shaukat Sultan insisted there was no rift with the US.
"Pakistan is saying nothing different from what the US commander is saying. We also say that the foreign fighters in our tribal areas must surrender, otherwise they will be killed," Sultan said.
"Pakistan is saying nothing different from what the US commander is saying"
Maj Gen Shaukat Sultan,
spokesman, Pakistan Army
A two-week military operation in South Waziristan in March left more than 120 people dead, but failed to capture any top al-Qaida men.
Hundreds of fighters escaped the operation, and officials say they have moved to caves near the border with Afghanistan with light and heavy weapons.
The bloodshed and limited success of the offensive have persuaded the Pakistani government to opt for negotiations instead of brute force.
Islamabad now says it will let foreign fighters stay in the region if they eschew "terrorism" and agree to live peacefully.
So far, Pakistani authorities have released 141 of the 163 Pakistani and foreign suspects captured in the March operation, saying investigations have proved them innocent.
Some of the foreigners in the Wana area are Afghan refugees. Others are Central Asian and Arab veterans of the anti-Soviet war in Afghanistan in the 1980s who settled in Pakistan, often marrying into local families.